11:14 p.m.
Dear All,
Is it possible to delete a galaxy user or multiple users with a UI call
or an API call?
Thanks,
Oren
4:36 p.m.
On Nov 9, 2011, at 6:14 PM, Oren Livne wrote:
Dear All,
Is it possible to delete a galaxy user or multiple users with a UI call or an API call?
Hi Oren,
Deleting users via the API is not currently implemented, but it can be done under the
admin panel in the UI. Adding it to the API would likely be fairly trivial.
--nate
Thanks,
Oren
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4:41 p.m.
Dear Nate,
Thanks for your answer.
1. I could not find it in the admin panel in the UI. When I click on
"Manage users", I get the user list and can select users, but there is
no "Delete User" button.
2. Which call in the code deletes a user? I can then write my own API
method.
3. If I try to reset passwords for more than one user at a time, I get
the error trackback:
|TypeError: Odd-length string| URL:
http://128.135.107.157:8080/admin/reset_user_password
Module weberror.evalexception.middleware:*364* in |respond|
<http://128.135.107.157:8080/admin/reset_user_password#> view
<http://128.135.107.157:8080/admin/reset_user_password#>
|>> <http://128.135.107.157:8080/admin/reset_user_password#>app_iter *=*
self*.*application*(*environ*,* detect_start_response*)*|
Module paste.debug.prints:*98* in |__call__|
<http://128.135.107.157:8080/admin/reset_user_password#> view
<http://128.135.107.157:8080/admin/reset_user_password#>
|>> <http://128.135.107.157:8080/admin/reset_user_password#>environ*,*
self*.*app*)*|
Module paste.wsgilib:*539* in |intercept_output|
<http://128.135.107.157:8080/admin/reset_user_password#> view
<http://128.135.107.157:8080/admin/reset_user_password#>
|>> <http://128.135.107.157:8080/admin/reset_user_password#>app_iter *=*
application*(*environ*,* replacement_start_response*)*|
Module paste.recursive:*80* in |__call__|
<http://128.135.107.157:8080/admin/reset_user_password#> view
<http://128.135.107.157:8080/admin/reset_user_password#>
|>> <http://128.135.107.157:8080/admin/reset_user_password#>*return*
self*.*application*(*environ*,* start_response*)*|
Module paste.httpexceptions:*632* in |__call__|
<http://128.135.107.157:8080/admin/reset_user_password#> view
<http://128.135.107.157:8080/admin/reset_user_password#>
|>> <http://128.135.107.157:8080/admin/reset_user_password#>*return*
self*.*application*(*environ*,* start_response*)*|
Module galaxy.web.framework.base:*160* in |__call__|
<http://128.135.107.157:8080/admin/reset_user_password#> view
<http://128.135.107.157:8080/admin/reset_user_password#>
|>> <http://128.135.107.157:8080/admin/reset_user_password#>body *=*
method*(* trans*,* ****kwargs *)*|
Module galaxy.web.framework:*173* in |decorator|
<http://128.135.107.157:8080/admin/reset_user_password#> view
<http://128.135.107.157:8080/admin/reset_user_password#>
|>> <http://128.135.107.157:8080/admin/reset_user_password#>*return*
func*(* self*,* trans*,* ***args*,* ****kwargs *)*|
Module galaxy.web.base.controller:*2025* in |reset_user_password|
<http://128.135.107.157:8080/admin/reset_user_password#> view
<http://128.135.107.157:8080/admin/reset_user_password#>
|>> <http://128.135.107.157:8080/admin/reset_user_password#>user *=*
get_user*(* trans*,* user_id *)*|
Module galaxy.web.base.controller:*2413* in |get_user|
<http://128.135.107.157:8080/admin/reset_user_password#> view
<http://128.135.107.157:8080/admin/reset_user_password#>
|>> <http://128.135.107.157:8080/admin/reset_user_password#>id *=*
trans*.*security*.*decode_id*(* id *)*|
Module galaxy.web.security:*45* in |decode_id|
<http://128.135.107.157:8080/admin/reset_user_password#> view
<http://128.135.107.157:8080/admin/reset_user_password#>
|>> <http://128.135.107.157:8080/admin/reset_user_password#>*return*
int*(* self*.*id_cipher*.*decrypt*(* obj_id*.*decode*(* 'hex' *)*
*)**.*lstrip*(* "!" *)* *)*|
Module encodings.hex_codec:*42* in |hex_decode|
<http://128.135.107.157:8080/admin/reset_user_password#> view
<http://128.135.107.157:8080/admin/reset_user_password#>
|>> <http://128.135.107.157:8080/admin/reset_user_password#>output *=*
binascii*.*a2b_hex*(*input*)*|
*TypeError: Odd-length string*
4. A similar problem occurs when I try to delete multiple data libraries
under "Manage data libraries". One library deletion works, but multiple
yields an error message:
Invalid Library id (
df7a1f0c02a5b08e,0a248a1f62a0cc04,03501d7626bd192f,3f5830403180d620,2a56795cad3c7db3,417e33144b294c21,5a1cff6882ddb5b2,2d9035b3fc152403,4b187121143038ff,c9468fdb6dc5c5f1,1e8ab44153008be8,e85a3be143d5905b
) specifield.
Thanks so much in advance,
Oren
On 11/10/2011 10:36 AM, Nate Coraor wrote:
On Nov 9, 2011, at 6:14 PM, Oren Livne wrote:
> Dear All,
> Is it possible to delete a galaxy user or multiple users with a UI call or an API
call?
Hi Oren,
Deleting users via the API is not currently implemented, but it can be done under the
admin panel in the UI. Adding it to the API would likely be fairly trivial.
--nate
> Thanks,
> Oren
> ___________________________________________________________
> Please keep all replies on the list by using "reply all"
> in your mail client. To manage your subscriptions to this
> and other Galaxy lists, please use the interface at:
>
> http://lists.bx.psu.edu/
5:17 p.m.
On Nov 10, 2011, at 11:41 AM, Oren Livne wrote:
Dear Nate,
Thanks for your answer.
1. I could not find it in the admin panel in the UI. When I click on "Manage
users", I get the user list and can select users, but there is no "Delete
User" button.
Hi Oren,
Hrm, it looks like the option to delete users was removed from the interface since it
couldn't be made conditional on a configuration setting (due to a limitation in
Galaxy's "Grids" feature, which is used to display the table of users in the
UI). They can be added by uncommented lines 98-100 in
lib/galaxy/web/controllers/admin.py:
#operations.append( grids.GridOperation( "Delete", condition=( lambda item:
not item.deleted ), allow_multiple=True ) )
#operations.append( grids.GridOperation( "Undelete", condition=( lambda
item: item.deleted and not item.purged ), allow_multiple=True ) )
#operations.append( grids.GridOperation( "Purge", condition=( lambda item:
item.deleted and not item.purged ), allow_multiple=True ) )
2. Which call in the code deletes a user? I can then write my own API
method.
mark_user_deleted() in lib/galaxy/web/base/controller.py. The preferred method for
implementing API methods is by moving the code in the web UI controller which performs the
actual action to lib/galaxy/actions/ and then changing the API and UI methods to call that
method. See the implementation of the Quota API for a reference.
3. If I try to reset passwords for more than one user at a time, I
get the error trackback:
TypeError: Odd-length string URL: http://128.135.107.157:8080/admin/reset_user_password
Module weberror.evalexception.middleware:364 in respond <plus.jpg> view
>> app_iter = self.application(environ, detect_start_response)
Module paste.debug.prints:98 in __call__ <plus.jpg> view
>> environ, self.app)
Module paste.wsgilib:539 in intercept_output <plus.jpg> view
>> app_iter = application(environ, replacement_start_response)
Module paste.recursive:80 in __call__ <plus.jpg> view
>> return self.application(environ, start_response)
Module paste.httpexceptions:632 in __call__ <plus.jpg> view
>> return self.application(environ, start_response)
Module galaxy.web.framework.base:160 in __call__ <plus.jpg> view
>> body = method( trans, **kwargs )
Module galaxy.web.framework:173 in decorator <plus.jpg> view
>> return func( self, trans, *args, **kwargs )
Module galaxy.web.base.controller:2025 in reset_user_password <plus.jpg>
view
>> user = get_user( trans, user_id )
Module galaxy.web.base.controller:2413 in get_user <plus.jpg> view
>> id = trans.security.decode_id( id )
Module galaxy.web.security:45 in decode_id <plus.jpg> view
>> return int( self.id_cipher.decrypt( obj_id.decode( 'hex' ) ).lstrip(
"!" ) )
Module encodings.hex_codec:42 in hex_decode <plus.jpg> view
>> output = binascii.a2b_hex(input)
TypeError: Odd-length string
4. A similar problem occurs when I try to delete multiple data libraries under
"Manage data libraries". One library deletion works, but multiple yields an
error message:
Invalid Library id (
df7a1f0c02a5b08e,0a248a1f62a0cc04,03501d7626bd192f,3f5830403180d620,2a56795cad3c7db3,417e33144b294c21,5a1cff6882ddb5b2,2d9035b3fc152403,4b187121143038ff,c9468fdb6dc5c5f1,1e8ab44153008be8,e85a3be143d5905b
) specifield.
Thanks for reporting these, we'll fix them as soon as possible. I've created a
bitbucket here to track them:
https://bitbucket.org/galaxy/galaxy-central/issue/678/some-user-and-libra...
--nate
Thanks so much in advance,
Oren
On 11/10/2011 10:36 AM, Nate Coraor wrote:
> On Nov 9, 2011, at 6:14 PM, Oren Livne wrote:
>
>
>> Dear All,
>> Is it possible to delete a galaxy user or multiple users with a UI call or an API
call?
>>
> Hi Oren,
>
> Deleting users via the API is not currently implemented, but it can be done under the
admin panel in the UI. Adding it to the API would likely be fairly trivial.
>
> --nate
>
>
>> Thanks,
>> Oren
>> ___________________________________________________________
>> Please keep all replies on the list by using "reply all"
>> in your mail client. To manage your subscriptions to this
>> and other Galaxy lists, please use the interface at:
>>
>>
>> http://lists.bx.psu.edu/
6:40 p.m.
Dear Nate,
Uncommenting those three lines worked. I also tried to implement a
change to the Grids feature that would allow injecting app.config into
Grids, but this doesn't work yet. (Are all variables such as operations
and standard_filters read and used by the framework as static vars even
before a UserListGrid object is created?)
I can now see the Delete, Undelete and Purge buttons. Is there a way to
permanently delete a user from the database? What does the purge feature do?
Thanks so much,
Oren
Hi Oren,
Hrm, it looks like the option to delete users was removed from the interface since it
couldn't be made conditional on a configuration setting (due to a limitation in
Galaxy's "Grids" feature, which is used to display the table of users in the
UI). They can be added by uncommented lines 98-100 in
lib/galaxy/web/controllers/admin.py:
#operations.append( grids.GridOperation( "Delete", condition=( lambda
item: not item.deleted ), allow_multiple=True ) )
#operations.append( grids.GridOperation( "Undelete", condition=( lambda
item: item.deleted and not item.purged ), allow_multiple=True ) )
#operations.append( grids.GridOperation( "Purge", condition=( lambda item:
item.deleted and not item.purged ), allow_multiple=True ) )
9:48 p.m.
On Nov 10, 2011, at 1:40 PM, Oren Livne wrote:
Dear Nate,
Uncommenting those three lines worked. I also tried to implement a change to the Grids
feature that would allow injecting app.config into Grids, but this doesn't work yet.
(Are all variables such as operations and standard_filters read and used by the framework
as static vars even before a UserListGrid object is created?)
Hi Oren,
Unfortunately, I'm not familiar enough with Grids to be able to answer this off the
top of my head.
I can now see the Delete, Undelete and Purge buttons. Is there a way
to permanently delete a user from the database? What does the purge feature do?
There's no way to do this from the Galaxy application, since it breaks one of
Galaxy's goals of permanence and reproducibility. There are quite a few references to
user records in other tables, so deleting the user would leave these dangling.
Purging a user removes all of the user's saved data from the instance.
--nate
Thanks so much,
Oren
> Hi Oren,
>
> Hrm, it looks like the option to delete users was removed from the interface since it
couldn't be made conditional on a configuration setting (due to a limitation in
Galaxy's "Grids" feature, which is used to display the table of users in the
UI). They can be added by uncommented lines 98-100 in
lib/galaxy/web/controllers/admin.py:
>
> #operations.append( grids.GridOperation( "Delete", condition=( lambda
item: not item.deleted ), allow_multiple=True ) )
> #operations.append( grids.GridOperation( "Undelete", condition=( lambda
item: item.deleted and not item.purged ), allow_multiple=True ) )
> #operations.append( grids.GridOperation( "Purge", condition=( lambda
item: item.deleted and not item.purged ), allow_multiple=True ) )
>
10:07 p.m.
On Nov 10, 2011, at 4:48 PM, Nate Coraor wrote:
On Nov 10, 2011, at 1:40 PM, Oren Livne wrote:
> Dear Nate,
>
> Uncommenting those three lines worked. I also tried to implement a change to the
Grids feature that would allow injecting app.config into Grids, but this doesn't work
yet. (Are all variables such as operations and standard_filters read and used by the
framework as static vars even before a UserListGrid object is created?)
Hi Oren,
Unfortunately, I'm not familiar enough with Grids to be able to answer this off the
top of my head.
The best approach for doing this is to change grid attributes in a method whose signature
includes trans ( so you have access to things like trans.app, etc ) before the method
renders the grid. Using this approach, we should be able to check a config setting before
rendering the UserLisGrid so that the delete / purge Grid operations are rendered based on
the config setting (rather than being commented out ). The current code in the
UserListGrid is very old and needs updating in this way. I am in the middle of other
stuff currently, but I'll try to take a look at this shortly ( unless other get a
chance first ).
Greg Von Kuster
Galaxy Development Team
greg(a)bx.psu.edu
12:26 a.m.
This issue has been corrected in change set 6261:26da65326612. The config setting
"allow_user_deletion" in universe_wsgi.ini must be set to true for the operation
buttons to be rendered.
On Nov 10, 2011, at 5:07 PM, Greg Von Kuster wrote:
On Nov 10, 2011, at 4:48 PM, Nate Coraor wrote:
> On Nov 10, 2011, at 1:40 PM, Oren Livne wrote:
>
>> Dear Nate,
>>
>> Uncommenting those three lines worked. I also tried to implement a change to the
Grids feature that would allow injecting app.config into Grids, but this doesn't work
yet. (Are all variables such as operations and standard_filters read and used by the
framework as static vars even before a UserListGrid object is created?)
>
> Hi Oren,
>
> Unfortunately, I'm not familiar enough with Grids to be able to answer this off
the top of my head.
>
The best approach for doing this is to change grid attributes in a method whose signature
includes trans ( so you have access to things like trans.app, etc ) before the method
renders the grid. Using this approach, we should be able to check a config setting before
rendering the UserLisGrid so that the delete / purge Grid operations are rendered based on
the config setting (rather than being commented out ). The current code in the
UserListGrid is very old and needs updating in this way. I am in the middle of other
stuff currently, but I'll try to take a look at this shortly ( unless other get a
chance first ).
Greg Von Kuster
Galaxy Development Team
greg(a)bx.psu.edu
3843
days inactive
3845
days old
galaxy-dev@lists.galaxyproject.org
7 comments
3 participants
participants (3)
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Greg Von Kuster -
Nate Coraor -
Oren Livne